The 2.2 Å resolution structure of the catalase-peroxidase KatG fromSynechococcus elongatusPCC7942

Abstract

The crystal structure of catalase-peroxidase from Synechococcus elongatus PCC7942 (SeKatG) was solved by molecular replacement and refined to an Rwork of 16.8% and an Rfree of 20.6% at 2.2 Å resolution. The asymmetric unit consisted of only one subunit of the catalase-peroxidase molecule, including a protoporphyrin IX haem moiety and two sodium ions. A typical KatG covalent adduct was formed, Met248-Tyr222-Trp94, which is a key structural element for catalase activity. The crystallographic equivalent subunit was created by a twofold symmetry operation to form the functional dimer. The overall structure of the dimer was quite similar to other KatGs. One sodium ion was located close to the proximal Trp314. The location and configuration of the proximal cation site were very similar to those of typical peroxidases such as ascorbate peroxidase. These features may provide a structural basis for the behaviour of the radical localization/delocalization during the course of the enzymatic reaction.

The crystal structure of isoniazid‐bound KatG catalase‐peroxidase from Synechococcus elongatus PCC7942

“…Although the electron density for Se KatG was mostly continuous and of high quality, the densities for the N‐terminal segment (residues 1–10) were poorly defined; accordingly, these residues were not included in the model. When the structure of INH‐bound Se KatG was superposed on that of substrate‐free Se KatG , no significant structural changes were observed in the enzyme; the rmsd for the C α atoms was 0.15 Å.…”

“…Crystals of INH‐bound Se KatG were nearly isomorphous with those of native KatG, and the structure of INH‐bound Se KatG was determined with the structure of native KatG (Protein Data Bank ID: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=3WNU) as a model . The structure was subjected to rigid‐body refinement from 25‐Å to 3.0‐Å resolution with refmac 5 from the ccp 4 package .…”

“…Extensive structural studies of KatGs from several bacteria have been performed; the crystal structures of KatG from Haloarcula marismortui , Burkholderia pseudomallei ( Bp KatG) , M. tuberculosis ( Mt KatG) and Synechococcus elongatus PCC7942 ( Se KatG) have been determined. However, an INH‐bound structure has only been reported for Bp KatG .…”

Crystal structure of the catalase–peroxidase KatG W78F mutant from Synechococcus elongatus PCC7942 in complex with the antitubercular pro‐drug isoniazid

“…In the case of the INH‐free wild‐type Se KatG (Fig. 2B) [17] and INH‐bound wild‐type Se KatG (Fig. 2C) [14], the map around the heme propionate moiety clearly showed that water molecules occupied in this space.…”

“…The mechanisms of INH activation have been explored not only in M. tuberculosis KatG (MtKatG) [5][6][7] but also in other KatGs such as those of Burkholderia pseudomallei (BpKatG) [4,[8][9][10], Synechocytis PCC 6803 (SynKatG) [11][12][13] and Synechococcus elongatus PCC7942 (SeKatG) [14]. These KatGs share at least 54% sequence identity, and their overall structures are very similar [15][16][17]. In addition, the configuration of the residues around the heme, including the unique covalent bonds among the side chains of the Met-Tyr-Trp residues of KatG, located on the distal side of the heme, are found in KatG proteins from all three species.…”